| NAME | RUSH YDS | GP | ATT | YPC | RUSH YDS/G | RUSH TD | REC YDS | REC | TRG | AVG | REC YDS/G | REC TD | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
 | Frank Gore | 11,073 | 148 | 2,442 | 4.5 | 74.8 | 64 | 2,883 | 342 | 502 | 8.4 | 19.5 | 11 |
 | Joe Perry | 7,344 | 131 | 1,475 | 5.0 | 56.1 | 50 | 1,280 | 185 | 6.9 | 9.8 | 7 | |
| Roger Craig | 7,064 | 121 | 1,686 | 4.2 | 58.4 | 50 | 4,442 | 508 | 8.7 | 36.7 | 16 | |
| Ken Willard | 5,930 | 125 | 1,582 | 3.7 | 47.4 | 45 | 2,156 | 273 | 7.9 | 17.2 | 16 | |
| Garrison Hearst | 5,535 | 73 | 1,189 | 4.7 | 75.8 | 26 | 1,604 | 174 | 162 | 9.2 | 22.0 | 7 |
| J.D. Smith | 4,370 | 97 | 1,007 | 4.3 | 45.1 | 37 | 1,109 | 121 | 9.2 | 11.4 | 5 | |
| Hugh McElhenny | 4,288 | 97 | 877 | 4.9 | 44.2 | 35 | 2,666 | 195 | 13.7 | 27.5 | 15 | |
| Kevan Barlow | 3,614 | 72 | 891 | 4.1 | 50.2 | 24 | 1,143 | 137 | 180 | 8.3 | 15.9 | 3 |
 | Steve Young | 3,581 | 150 | 608 | 5.9 | 23.9 | 37 | 2 | 2 | 0 | 1.0 | 0.0 | 0 |
| Wendell Tyler | 3,112 | 48 | 624 | 5.0 | 64.8 | 17 | 669 | 82 | 8.2 | 13.9 | 6 | |
| Delvin Williams | 2,966 | 54 | 669 | 4.4 | 54.9 | 20 | 841 | 82 | 10.3 | 15.6 | 5 | |
| Wilbur Jackson | 2,955 | 72 | 745 | 4.0 | 41.0 | 10 | 1,233 | 148 | 8.3 | 17.1 | 3 | |
| Ricky Watters | 2,840 | 43 | 653 | 4.3 | 66.0 | 25 | 1,450 | 140 | 10.4 | 33.7 | 8 | |
 | Carlos Hyde | 2,729 | 50 | 655 | 4.2 | 54.6 | 21 | 634 | 109 | 152 | 5.8 | 12.7 | 3 |
 | Christian McCaffrey | 2,407 | 31 | 481 | 5.0 | 77.6 | 20 | 1,174 | 134 | 167 | 8.8 | 37.9 | 11 |
| Charlie Garner | 2,371 | 32 | 499 | 4.8 | 74.1 | 11 | 1,182 | 124 | 170 | 9.5 | 36.9 | 5 |
 | Colin Kaepernick | 2,300 | 69 | 375 | 6.1 | 33.3 | 13 | 0 | 0 | 0 | 0.0 | 0 | |
 | Matt Breida | 1,902 | 43 | 381 | 5.0 | 44.2 | 6 | 561 | 67 | 89 | 8.4 | 13.0 | 4 |
| Tom Rathman | 1,902 | 115 | 516 | 3.7 | 16.5 | 26 | 2,490 | 294 | 8.5 | 21.7 | 8 | |
| Vic Washington | 1,813 | 40 | 483 | 3.8 | 45.3 | 14 | 948 | 112 | 8.5 | 23.7 | 5 | |
| Paul Hofer | 1,746 | 77 | 416 | 4.2 | 22.7 | 16 | 1,634 | 147 | 11.1 | 21.2 | 5 | |
| Larry Schreiber | 1,734 | 60 | 502 | 3.5 | 28.9 | 10 | 966 | 116 | 8.3 | 16.1 | 4 | |
 | Jeff Wilson Jr. | 1,733 | 45 | 390 | 4.4 | 38.5 | 15 | 387 | 45 | 69 | 8.6 | 8.6 | 4 |
 | Raheem Mostert | 1,610 | 46 | 284 | 5.7 | 35.0 | 11 | 361 | 36 | 48 | 10.0 | 7.8 | 3 |
 | Joe Montana | 1,595 | 167 | 414 | 3.9 | 9.6 | 20 | 0 | 0 | 0.0 | 0 | ||
| Jeff Garcia | ||||||||||||
 | Elijah Mitchell | ||||||||||||
| Doug Cunningham | ||||||||||||
| John David Crow | ||||||||||||
| Gary Lewis | ||||||||||||
 | Jordan Mason | ||||||||||||
| Terry Kirby | ||||||||||||
| Kendall Hunter | ||||||||||||
| John Brodie | ||||||||||||
| Earl Cooper | ||||||||||||
 | Deebo Samuel | ||||||||||||
| Billy Kilmer | ||||||||||||
 | O.J. Simpson | ||||||||||||
| Derek Loville | ||||||||||||
| John Henry Johnson | ||||||||||||
| Dexter Carter | ||||||||||||
| Joe Arenas | ||||||||||||
| Johnny Strzykalski | ||||||||||||
| William Floyd | ||||||||||||
| Joe Cribbs | ||||||||||||
| Maurice Hicks | ||||||||||||
| Jimmy Thomas | ||||||||||||
 | Alex Smith | ||||||||||||
| Bill Ring | ||||||||||||
| Bob Ferrell |
StatMuse has season-level data for rushing yards going back to the 1932 season.